12 ms·

> The tendency for friends to have similar genomes might result from people befriending those of similar ancestry, but the duo are confident that isn't the case

by choxi 9y ago

> The tendency for friends to have similar genomes might result from people befriending those of similar ancestry, but the duo are confident that isn't the case. Not only did they control for the effect of population structure and ancestry, but the Framingham data is relatively homogeneous in terms of ethnicity, consisting largely of people of European descent. How did they control it? Even amongst Europeans, I imagine French people are just more likely to have French friends.

anbende 9y ago
Agreed, and it's hard for me to see how you control ancestry or ethnic perfectly, since ethnicity is just a relatively stable form of genetic diversity. I might counter-hypothesize that the 1% they found is just the amount of variance in ethnic group that wasn't controlled for perfectly.
gph 9y ago
Framingham, MA is old school New England. I wouldn't be surprised if 75+% of the participants are of direct English/Anglo-Saxon descent, even though the article describes it as "European" descent.
- emodendroket 9y ago
  Even if it isn't, I don't think there is much meaningful distinction left among Americans of English and French ancestry. How many people would even notice?
  - gph 9y ago
    Depends on the area. I think in parts of Maine where there's a strong Quebecois influence there's definitely a meaningful distinction. There's other areas, especially in rural communities, where a specific European country has a lingering overstated influence. But within any major metro area you're right, there's typically little meaningful distinction anyone would pick up on between two Americans of different European ancestry.
    - emodendroket 9y ago
      Certainly that's strongest in New England. But I don't know most people are French-Canadian unless they tell me (especially given that intermarriage is pretty common so surnames aren't a reliable guide).
    - KGIII 9y ago
      I live in Maine. You are correct. They teach French in school, to everyone. Some areas have classes in French that are not specifically French learning classes. The majority of those living here without documentation are Canadians. If you get into cities like Lewiston, you'll find whole areas where French is commonly spoken. It's kinda neat, actually. I am also a citizen of Canada, but don't speak French. It's fun to learn and be exposed to the culture, but I digress.
    - interfixus 9y ago
      > there's typically little meaningful distinction anyone would pick up on We don't know. At least I don't. But it would hugely surprise me if we are not constantly picking up on all sorts of subtle gene expressions. And this needs not in any way be a conscious process. Sophisticated ability to suss out degrees of relatedness would be a far too useful feature not to have been selected for again and again and again.
      - emodendroket 9y ago
        I have two thoughts there: 1. Surely very high intermarriage rates between different European ethnicities complicate that. 2. In that case, wouldn't the opposite behavior be expected? If the goal were to have as little genetic variation as possible humans would be better off reproducing asexually.
        interfixus 9y ago
        > Surely very high intermarriage rates between different European ethnicities complicate that Very high intermarriage rates? Wherever did you pick up such an idea? > In that case, wouldn't the opposite behavior be expected? If the goal were to have as little genetic variation as possible humans would be better off reproducing asexually There is no 'goal'. And too little variation seems to be a universally bad idea. It is a simple, observablke fact that most of us stick to partners reminiscent of ourselves. We may argue about the reasons, but the thing itself is clear and obvious.
- QAPereo 9y ago
  Framingham is pretty much just like that, although it's less than 75% it's still a supermajority. https://datausa.io/profile/geo/framingham-ma/#demographics https://datausa.io/profile/geo/framingham-ma/#demographics
  - gph 9y ago
    Remember also that the dataset they are using began back in the 1940s when the towns demographics would have been much farther skewed towards English/Anglo-Saxon. And while they've included more participants over the course of the study, it's mainly been adding the descendants of the original participants.
    - QAPereo 9y ago
      Good points, but either way the go study is doubtful as hell.
- smitherfield 9y ago
  As someone who lives in the area, this is a ludicrous statement. Framingham has one of the proportionally-largest immigrant populations of anywhere in the state, and, by extension, New England. Statistics to the contrary are out-of-date or highly-misleading/inaccurate (counting Brazilians as "non-Hispanic white" and/or, for obvious reasons, undercounting illegal and non-English-speaking immigrants). Further the non-Hispanic white population is itself ethnically diverse (Italian, Portuguese, Irish etc) with "English/Anglo-Saxons" a small minority.
  - gph 9y ago
    Like I said below, the study this is based on started in 1940. Hence the 'old-school' New England.
eighthnate 9y ago
> How did they control it? Even amongst Europeans, I imagine French people are just more likely to have French friends. This study is in the US. By "people of european descent", they are referring to white americans rather than actual europeans. Also french is a linguist/national/ethnic classification rather than a genetic one.
Real_S 9y ago
Population structure is controlled through the use of the structure as a co-factor in the analyses. They use a principal component analysis on the genotypes to estimate the structure, and then use the first few principal components (PCs) as cofactors in the analyses. So if the European population they used consisted of half English and half French participants, then the first PC would likely divide the two. So if British or French ethnicity affected the analysis, this effect would be reduced or eliminated using just the first PC. How many PCs should be used? Well, ten is a common number chosen. Is it enough? Probably for most studies including this one. So ancestry and ethnicity in this type of research emerges purely from a PC analysis on the genotypes. They do not use self-reported ethnicity or any other type of common ethnic grouping. To control for population structure, self-reported ethnicity is rarely useful. Its far too unreliable. But these groupings do sometimes loosely correspond to the PCs found in the analysis, supporting the use of PC as a method to control for ethnicity.
- subroutine 9y ago
  Do you believe these findings though? (original article: http://www.pnas.org/content/111/Supplement_3/10796.full http://www.pnas.org/content/111/Supplement_3/10796.full ) To me there are a few things worth highlighting, that are at least tangentially relevant: 1. This article was a PNAS Direct Submission. PNAS Direct Submission, a privilege typically reserved for members of the National Academy of Sciences, is like using trump-card to basically skip peer review. Since NAS members are usually great scientists with a track-record of publishing in high-impact peer reviewed journals, PNAS Direct Submissions are usually saved for pet-projects where the underlying science is... mmmm... of dubious quality. This is not always the case, but when all-star scientists opt for PNAS DS, it's certainly a reason to be speculative. 2. Nick Christakis and James Fowler have teamed up for a number of fancy-ass studies (the type that ensure people will want to write wikipedia pages about them, and lead to TED talk invites); some suggesting personal attributes like obesity, smoking, and happiness arise via 'social contagion', that is, behavioral propensities are transmitted over social networks. And studies like this one, where they find friendship affinities embedded in the genome. 3. I recently read a genome-wide association study (GWAS) with over 400 authors (https://www.ncbi.nlm.nih.gov/pubmed/28714976 https://www.ncbi.nlm.nih.gov/pubmed/28714976). I think 400 authors is way above median, but even relatively tame GWAS typically require a group effort just for data QC. Here, somehow these two guys did it all themselves. 4. Not only did they find that some SNPs were positively correlated, they also found some that were negatively correlated... "Across the whole genome, friends’ genotypes at the single nucleotide polymorphism level tend to be positively correlated (homophilic). In fact, the increase in similarity relative to strangers is at the level of fourth cousins. However, certain genotypes are also negatively correlated (heterophilic) in friends. And the degree of correlation in genotypes can be used to create a “friendship score” that predicts the existence of friendship ties in a hold-out sample." So the HN/Nature title might as well be: "Friends are Genetically similar, and Genetically Different".

by choxi 9y ago

anbende 9y ago

Agreed, and it's hard for me to see how you control ancestry or ethnic perfectly, since ethnicity is just a relatively stable form of genetic diversity. I might counter-hypothesize that the 1% they found is just the amount of variance in ethnic group that wasn't controlled for perfectly.

gph 9y ago

Framingham, MA is old school New England. I wouldn't be surprised if 75+% of the participants are of direct English/Anglo-Saxon descent, even though the article describes it as "European" descent.

emodendroket 9y ago
Even if it isn't, I don't think there is much meaningful distinction left among Americans of English and French ancestry. How many people would even notice?
- gph 9y ago
  Depends on the area. I think in parts of Maine where there's a strong Quebecois influence there's definitely a meaningful distinction. There's other areas, especially in rural communities, where a specific European country has a lingering overstated influence. But within any major metro area you're right, there's typically little meaningful distinction anyone would pick up on between two Americans of different European ancestry.
  - emodendroket 9y ago
    Certainly that's strongest in New England. But I don't know most people are French-Canadian unless they tell me (especially given that intermarriage is pretty common so surnames aren't a reliable guide).
  - KGIII 9y ago
    I live in Maine. You are correct. They teach French in school, to everyone. Some areas have classes in French that are not specifically French learning classes. The majority of those living here without documentation are Canadians. If you get into cities like Lewiston, you'll find whole areas where French is commonly spoken. It's kinda neat, actually. I am also a citizen of Canada, but don't speak French. It's fun to learn and be exposed to the culture, but I digress.
  - interfixus 9y ago
    > there's typically little meaningful distinction anyone would pick up on We don't know. At least I don't. But it would hugely surprise me if we are not constantly picking up on all sorts of subtle gene expressions. And this needs not in any way be a conscious process. Sophisticated ability to suss out degrees of relatedness would be a far too useful feature not to have been selected for again and again and again.
    - emodendroket 9y ago
      I have two thoughts there: 1. Surely very high intermarriage rates between different European ethnicities complicate that. 2. In that case, wouldn't the opposite behavior be expected? If the goal were to have as little genetic variation as possible humans would be better off reproducing asexually.
      - interfixus 9y ago
        > Surely very high intermarriage rates between different European ethnicities complicate that Very high intermarriage rates? Wherever did you pick up such an idea? > In that case, wouldn't the opposite behavior be expected? If the goal were to have as little genetic variation as possible humans would be better off reproducing asexually There is no 'goal'. And too little variation seems to be a universally bad idea. It is a simple, observablke fact that most of us stick to partners reminiscent of ourselves. We may argue about the reasons, but the thing itself is clear and obvious.
QAPereo 9y ago
Framingham is pretty much just like that, although it's less than 75% it's still a supermajority. https://datausa.io/profile/geo/framingham-ma/#demographics https://datausa.io/profile/geo/framingham-ma/#demographics
- gph 9y ago
  Remember also that the dataset they are using began back in the 1940s when the towns demographics would have been much farther skewed towards English/Anglo-Saxon. And while they've included more participants over the course of the study, it's mainly been adding the descendants of the original participants.
  - QAPereo 9y ago
    Good points, but either way the go study is doubtful as hell.
smitherfield 9y ago
As someone who lives in the area, this is a ludicrous statement. Framingham has one of the proportionally-largest immigrant populations of anywhere in the state, and, by extension, New England. Statistics to the contrary are out-of-date or highly-misleading/inaccurate (counting Brazilians as "non-Hispanic white" and/or, for obvious reasons, undercounting illegal and non-English-speaking immigrants). Further the non-Hispanic white population is itself ethnically diverse (Italian, Portuguese, Irish etc) with "English/Anglo-Saxons" a small minority.
- gph 9y ago
  Like I said below, the study this is based on started in 1940. Hence the 'old-school' New England.

eighthnate 9y ago

> How did they control it? Even amongst Europeans, I imagine French people are just more likely to have French friends. This study is in the US. By "people of european descent", they are referring to white americans rather than actual europeans. Also french is a linguist/national/ethnic classification rather than a genetic one.

Real_S 9y ago

Population structure is controlled through the use of the structure as a co-factor in the analyses. They use a principal component analysis on the genotypes to estimate the structure, and then use the first few principal components (PCs) as cofactors in the analyses. So if the European population they used consisted of half English and half French participants, then the first PC would likely divide the two. So if British or French ethnicity affected the analysis, this effect would be reduced or eliminated using just the first PC. How many PCs should be used? Well, ten is a common number chosen. Is it enough? Probably for most studies including this one. So ancestry and ethnicity in this type of research emerges purely from a PC analysis on the genotypes. They do not use self-reported ethnicity or any other type of common ethnic grouping. To control for population structure, self-reported ethnicity is rarely useful. Its far too unreliable. But these groupings do sometimes loosely correspond to the PCs found in the analysis, supporting the use of PC as a method to control for ethnicity.

subroutine 9y ago
Do you believe these findings though? (original article: http://www.pnas.org/content/111/Supplement_3/10796.full http://www.pnas.org/content/111/Supplement_3/10796.full ) To me there are a few things worth highlighting, that are at least tangentially relevant: 1. This article was a PNAS Direct Submission. PNAS Direct Submission, a privilege typically reserved for members of the National Academy of Sciences, is like using trump-card to basically skip peer review. Since NAS members are usually great scientists with a track-record of publishing in high-impact peer reviewed journals, PNAS Direct Submissions are usually saved for pet-projects where the underlying science is... mmmm... of dubious quality. This is not always the case, but when all-star scientists opt for PNAS DS, it's certainly a reason to be speculative. 2. Nick Christakis and James Fowler have teamed up for a number of fancy-ass studies (the type that ensure people will want to write wikipedia pages about them, and lead to TED talk invites); some suggesting personal attributes like obesity, smoking, and happiness arise via 'social contagion', that is, behavioral propensities are transmitted over social networks. And studies like this one, where they find friendship affinities embedded in the genome. 3. I recently read a genome-wide association study (GWAS) with over 400 authors (https://www.ncbi.nlm.nih.gov/pubmed/28714976 https://www.ncbi.nlm.nih.gov/pubmed/28714976). I think 400 authors is way above median, but even relatively tame GWAS typically require a group effort just for data QC. Here, somehow these two guys did it all themselves. 4. Not only did they find that some SNPs were positively correlated, they also found some that were negatively correlated... "Across the whole genome, friends’ genotypes at the single nucleotide polymorphism level tend to be positively correlated (homophilic). In fact, the increase in similarity relative to strangers is at the level of fourth cousins. However, certain genotypes are also negatively correlated (heterophilic) in friends. And the degree of correlation in genotypes can be used to create a “friendship score” that predicts the existence of friendship ties in a hold-out sample." So the HN/Nature title might as well be: "Friends are Genetically similar, and Genetically Different".